This bug happens to me in the scorn guild (Guild of the Mailed Fist), not sure about any others but most likely.
The downstairs (not the hellhound unlocked one) has the door to the storage that is split by guild rank. The guard doesnt respond to anything, "say enter" doesnt work, nothing lets me get inside. Rank doesnt matter, i have tried as GuildMaster and as Master.
The Upstairs (Spectre unlocked floor), the rooms inside the upper floor are inaccessible. I have purchased every token buyable in the basement, yet only the first gate will open. Some of the other gates with the guards, you are able to say "say enter" and it will say "entry granted to ____" but you are still unable to enter the gate.The only room i am able to actually access is the room with the 4 levers, 3 of the reset levers and the 1 lever allowing guild members into the rooms. The Garden is also inaccessible and inside the toolshed, the "say enter" entry doesnt work, neither do the other two gates on the west and east end of the room. Everything else so far works.